Contacts of the strand formed by residues 156 - 166 (chain B) in PDB entry 3SJ5
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 156 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B LEU* 3.7 27.4 - - + -
95B LEU* 5.8 0.4 - - + -
145B ILE* 3.6 33.2 - - + +
146B GLU* 5.0 3.1 - - + -
149B SER* 3.8 24.1 + - - +
154B GLU 3.9 0.2 - - - +
155B GLU* 1.3 81.0 - - - +
157B SER* 1.3 59.7 + - - +
158B VAL* 3.8 14.8 - - + -
176B ILE* 3.9 13.2 - - + -
177B LYS 3.2 14.6 - - - +
178B PHE* 3.9 13.5 - - + -
179B LYS* 5.3 0.9 - - - +
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Residues in contact with SER 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ASN* 3.8 33.0 + - - -
156B ILE* 1.3 75.6 - - - +
158B VAL* 1.3 62.5 + - - +
159B GLU* 4.1 0.7 + - - +
175B ARG 3.6 1.4 - - - +
176B ILE* 3.4 5.4 - - - +
177B LYS* 2.9 56.0 + - - +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASN* 5.7 3.4 + - - +
64A ASN* 5.3 1.4 + - - -
68B ARG* 6.1 3.1 - - - +
142B LEU* 4.4 13.2 - - + -
145B ILE* 4.1 14.6 - - + -
146B GLU* 5.3 11.4 - - + +
156B ILE* 3.8 26.9 - - + -
157B SER* 1.3 79.2 - - - +
159B GLU* 1.3 62.1 + - - +
160B GLU* 4.2 4.9 + - + +
174B VAL* 3.8 34.3 - - + -
175B ARG 3.6 3.4 - - - +
176B ILE* 4.5 4.9 - - + -
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Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ASN* 6.0 1.8 - - - +
64A ASN* 3.3 33.6 + - - +
136A LYS* 5.6 5.9 + - - +
163A ARG* 5.6 1.8 - - - +
157B SER* 4.1 0.8 - - - +
158B VAL* 1.3 73.6 - - - +
160B GLU* 1.3 71.8 + - - +
161B VAL* 3.5 7.4 + - + +
174B VAL* 3.2 6.1 - - - -
175B ARG* 2.8 63.8 + - + +
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Residues in contact with GLU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A TYR* 4.9 2.4 - - - -
160A GLU* 4.0 8.0 - - - +
163A ARG* 2.9 53.9 + - - +
68B ARG* 4.8 7.3 + - - -
142B LEU* 3.7 22.5 - - + +
158B VAL* 4.1 4.1 + - + +
159B GLU* 1.3 77.6 - - - +
161B VAL* 1.3 60.2 + - - +
163B ARG* 3.3 26.1 + - + -
172B LEU* 4.4 11.0 - - + -
173B LYS 3.9 4.0 - - - -
174B VAL* 4.1 15.7 - - + -
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Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A TYR* 4.8 4.3 + - - -
163A ARG* 3.8 15.5 - - - +
164A GLY* 4.0 6.9 - - - -
165A GLU* 6.0 0.5 - - - +
128B GLU* 5.5 5.2 - - - +
159B GLU* 3.9 18.8 - - + +
160B GLU* 1.3 74.4 - - - +
162B GLU* 1.3 74.4 + - + +
173B LYS* 2.9 31.1 + - + +
174B VAL 4.3 2.0 - - - -
175B ARG* 4.0 22.4 - - + +
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Residues in contact with GLU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ARG* 3.3 14.1 - - - +
164A GLY* 4.5 7.8 - - - -
165A GLU 5.1 4.0 + - - +
130B GLU* 4.7 4.0 - - - +
160B GLU 3.8 0.4 - - - -
161B VAL* 1.3 95.9 - - + +
163B ARG* 1.3 61.4 + - - +
171B ARG 4.4 0.7 - - - -
172B LEU* 3.2 10.4 - - - +
173B LYS* 2.8 64.7 + - + -
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Residues in contact with ARG 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLU* 5.6 1.8 - - - +
160A GLU* 3.0 51.3 + - - +
161A VAL 3.8 13.5 - - - +
162A GLU* 3.3 4.4 - - - +
163A ARG* 2.9 41.2 + - + +
138B TYR* 3.4 49.1 - - + +
139B ASP* 5.0 8.5 + - - -
142B LEU* 4.2 14.8 - - - +
160B GLU* 3.3 25.3 + - - -
162B GLU* 1.3 76.9 - - - +
164B GLY* 1.3 63.1 + - - +
171B ARG 3.3 7.0 - - - +
172B LEU* 4.0 14.2 - - + +
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Residues in contact with GLY 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A VAL 4.0 10.5 - - - -
162A GLU* 4.4 7.6 - - - -
138B TYR* 3.7 0.4 + - - -
163B ARG* 1.3 78.0 - - - +
165B GLU* 1.3 73.2 + - - +
166B LYS* 5.2 0.8 - - - +
171B ARG* 2.9 37.7 + - - +
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Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A VAL* 4.6 6.7 - - + +
162A GLU* 5.2 7.2 + - + +
136B LYS* 3.2 22.2 + - - +
138B TYR* 2.6 27.5 + - - -
164B GLY* 1.3 75.7 - - - -
166B LYS* 1.3 62.9 + - - +
168B GLY* 5.3 4.0 - - - +
169B PHE 3.3 8.7 - - - +
170B SER* 2.5 26.6 + - - -
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Residues in contact with LYS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B GLY 4.1 0.6 + - - +
165B GLU* 1.3 76.9 - - - +
167B ASP* 1.3 88.7 + - - +
168B GLY 3.1 0.7 - - - -
169B PHE* 2.8 27.5 + - - +
171B ARG* 4.3 29.1 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il